Reads Manipulation

sickle
Function: Sickle is a tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. It will also discard reads based upon the length threshold. It takes the quality values and slides a window across them whose length is 0.1 times the length of the read. If this length is less than 1, then the window is set to be equal to the length of the read. Otherwise, the window slides along the quality values until the average quality in the window rises above the threshold, at which point the algorithm determines where within the window the rise occurs and cuts the read and quality there for the 5'-end cut. Then when the average quality in the window drops below the threshold, the algorithm determines where in the window the drop occurs and cuts both the read and quality strings there for the 3'-end cut. However, if the length of the remaining sequence is less than the minimum length threshold, then the read is discarded entirely (or replaced with an "N" record). 5'-end trimming can be disabled.
Usage: sickle pe -t [solexa|illumina|sanger] -f forward_reads.fastq -r reverse_reads.fastq -o trimmed_output_file1.fastq -p trimmed_output_file2.fastq -s trimmed_singles_file.fastq
cd-hit-dup
Function: cd-hit-dup is a simple tool for removing duplicates from sequencing reads, with optional step to detect and remove chimeric reads.
Usage: cd-hit-dup -i input.fa -o output.fa [other options]
maq fasta2bfa
Function: Convert sequences in FASTA format to Maq’s BFA (binary FASTA) format.
Usage: maq fasta2bfa in.ref.fasta out.ref.bfa
insertion_profile.py
Function: Calculate the distributions of inserted nucleotides across reads.
Usage: insertion_profile.py -s "PE" -i test.bam -o out
CAP3
Function: CAP3 (Contig Assembly Program) is a DNA sequence assembly program for small-scale assembly with or without quality values.
Usage: cap3 input_reads.fasta [options] > output.txt
cd-hit-dup
Function: cd-hit-dup is a simple tool for removing duplicates from sequencing reads, with optional step to detect and remove chimeric reads. A number of options are provided to tune how the duplicates are removed.
Usage: cd-hit-dup -i input.fa -o output
maq sol2sanger
Function: Convert Solexa FASTQ to standard/Sanger FASTQ format.
Usage: maq sol2sanger in.sol.fastq out.sanger.fastq
bamPEFragmentSize
Function: This tool samples the given BAM files with paired-end data to estimate the fragment length distribution. Properly paired reads are preferred for computation, i.e., unless a region does not contain any concordant pairs, discordant pairs are ignored.
Usage: bamPEFragmentSize [-h] [--bamfiles bam files [bam files ...]] [--histogram FILE] [--plotFileFormat FILETYPE] [--numberOfProcessors INT] [--samplesLabel SAMPLESLABEL [SAMPLESLABEL ...]] [--plotTitle PLOTTITLE] [--maxFragmentLength MAXFRAGMENTLENGTH] [--logScale] [--binSize INT] [--distanceBetweenBins INT] [--blackListFileName BED file] [--table FILE] [--outRawFragmentLengths FILE] [--verbose] [--version]
Kraken-report
Function: This tool is designed to translate results of the Kraken metagenomic classifier (see citations below) to the full representation of NCBI taxonomy.
Usage: kraken-report --db $DBNAME kraken.output
read_GC.py
Function: GC content distribution of reads.
Usage: read_GC.py -i Pairend_nonStrandSpecific_36mer_Human_hg19.bam -o output
geneBody_coverage.py
Function: Calculate the RNA-seq reads coverage over gene body.
Usage: geneBody_coverage.py -r hg19.housekeeping.bed -i /data/alignment/ -o output
PRINSEQ
Function: PRINSEQ is a tool that generates summary statistics of sequence and quality data and that is used to filter, reformat and trim next-generation sequence data. It is particular designed for 454/Roche data, but can also be used for other types of sequence data. PRINSEQ is available through a user-friendly web interface or as standalone version. The standalone version is primarily designed for data preprocessing and does not generate summary statistics in graphical form.
Usage: prinseq-lite.pl [-fasta|-fastq] input_reads_pair_1.[fasta|fastq] [-fasta2|-fastq2] input_reads_pair_2.[fasta|fastq] -out_format [1|2|3|4|5] [options]
Kraken
Function: Kraken is a taxonomic sequence classifier that assigns taxonomic labels to short DNA reads.
Usage: kraken --db $DBNAME seqs.fa
clipping_profile.py
Function: Calculate the distributions of clipped nucleotides across reads
Usage: clipping_profile.py -i Pairend_StrandSpecific_51mer_Human_hg19.bam -s "PE" -o out
Kraken-filter
Function: At present, we have not yet developed a confidence score with a solid probabilistic interpretation for Kraken. However, we have developed a simple scoring scheme that has yielded good results for us, and we've made that available in the kraken-filter script. The approach we use allows a user to specify a threshold score in the [0,1] interval; the kraken-filter script then will adjust labels up the tree until the label's score (described below) meets or exceeds that threshold. If a label at the root of the taxonomic tree would not have a score exceeding the threshold, the sequence is called unclassified by kraken-filter.
Usage: kraken-filter --db $DBNAME [--threshold NUM] kraken.output